Cardiac MRI

Cine cardiovascular magnetic resonance (CMR) analysis relies on multi-frame sequences capturing the full cardiac cycle. However, standard multi-frame acquisition depends heavily on electrocardiogram (ECG) gating and repeated breath-holds, posing challenges in uncooperative populations, resource-limited settings, and temporally corrupted datasets. Existing methods that synthesize full cardiac sequences either rely on explicit ECG signals to parameterize myocardium function, or employ deformable registration without physiological constraints, failing to faithfully reproduce clinically relevant dynamic metrics such as ejection fraction (EF) and ventricular contraction magnitude. We present PhaseFlow, a unified generative framework that overcomes both limitations. PhaseFlow estimates a non-linear cardiac phase signal directly from the input sequence via a segmentation-derived left-ventricular (LV) area curve, capturing the asymmetric dynamics of systole and diastole without any ECG dependency. At inference, this phase signal is provided by a pathology-specific template, informing phase-specific frame generation. A rectified flow model conditioned on the phase and slice position synthesizes the full cardiac motion trajectory in the latent space, decoded into a diffeomorphic displacement field that warps end-diastole pixel intensities directly, eliminating the reconstruction blur often accompanying the variational autoencoder. On the ACDC benchmark, PhaseFlow achieves superior physiological fidelity and image realism, with best LV volume curve $R^2$, structural similarity (SSIM) and generative quality (FID) among all baselines. Ablation studies confirm that each proposed component contributes measurably to the overall performance.

Cine cardiovascular magnetic resonance (CMR) captures the cardiac cycle as a four-dimensional (4D) sequence, but standard acquisition requires electrocardiogram (ECG) gating and repeated breath holds. Visual realism alone does not establish accurate patient-specific ejection fraction (EF) or ventricular volumes. We present PhaseFlow3D, a generative framework that synthesizes a complete 4D cine sequence from a single end-diastolic (ED) three-dimensional (3D) volume without ECG. To capture asymmetric systolic and diastolic dynamics, it represents the cardiac cycle as a piecewise linear phase anchored at ED and end-systolic (ES) time points. At inference, a population-level canonical template supplies this phase without patient-specific temporal information. A phase-conditioned rectified flow model generates a cardiac motion trajectory in latent space. Radial Contraction Decomposition converts each latent state into a 3D displacement field, combining a physics-informed radial component for centripetal myocardial contraction with an image-conditioned residual for rotation and out-of-plane motion. Each frame is generated by directly warping the ED volume, bypassing variational autoencoder decoding. On the combined ACDC and M&Ms benchmark, PhaseFlow3D achieves the lowest EF mean absolute error, the only positive left-ventricular volume-curve $R^2$, and the best distributional quality among compared methods. Ablations confirm each component's contribution. Downstream evaluations demonstrate the utility of the synthesized sequences and displacement fields for segmentation, pathology classification, label propagation, and myocardial strain analysis.

Cardiac magnetic resonance imaging reconstruction aims to recover high-quality images from undersampled acquisitions, enabling faster scans while preserving diagnostic fidelity. Recent reconstruction methods are typically trained from scratch and often require large amounts of task-specific data, limiting their robustness under data scarcity and distribution shifts. In this work, we investigate whether pretrained vision foundation models can serve as effective priors for accelerated cardiac MRI reconstruction. We propose a reconstruction framework that integrates frozen and parameter-efficiently adapted visual encoders, including CLIP, BiomedCLIP, and DINOv2, within a transformer-based reconstruction architecture. Extensive experiments on the CMRxRecon2023 and CMRxRecon2024 benchmarks demonstrate that pretrained representations consistently outperform a transformer trained from scratch across multiple acceleration factors. We further evaluate performance under limited supervision and cross-dataset transfer, showing that foundation models provide superior data efficiency and generalization. While frozen representations are particularly effective in extreme low-data regimes, Low-Rank Adaptation (LoRA) yields additional gains when moderate amounts of training data are available. Among the evaluated backbones, DINOv2 achieves the strongest overall performance. These findings highlight the potential of vision foundation models as robust and transferable priors for cardiac MRI reconstruction.

Three-dimensional (3D) left ventricular (LV) reconstruction from sparse cardiac magnetic resonance (CMR) imaging remains challenging due to inter-slice misalignment and insufficient local spatial information between slices. Global aggregation of contour features may obscure local contour-to-surface relationships. We propose Local2Mesh, a spatially localized contour-to-mesh framework that deforms a template mesh to reconstruct 3D LV geometry from sparse 2D contours without 3D mesh annotations. The framework introduces geometry-aware alignment to correct inter-slice misalignment and a plane-aware Local Router that routes contour features to template vertices using vertex-to-plane distances. Local and global contour features then jointly guide graph-based template deformation for 3D LV reconstruction. Experiments on two public datasets, M&Ms-2 and ACDC, demonstrate superior geometric reconstruction and functional estimation over existing methods. Zero-shot transfer from M&Ms-2 to ACDC demonstrates strong cross-dataset generalization. Reconstructed meshes also improve disease classification over sparse contours, supporting their utility for downstream cardiac analysis. These results demonstrate that combining geometry-aware alignment with local contour-to-vertex modeling improves LV reconstruction from sparse 2D contours and supports downstream cardiac analysis. The code is available at https://github.com/hwu918945-alt/loca2mesh.

Cardiovascular magnetic resonance (CMR), including cine imaging, is a reference standard for the noninvasive assessment of cardiac morphology and ventricular function. Cine CMR interpretation integrates qualitative visual assessment with quantitative measurements of ventricular volumes, ejection fraction, myocardial mass, wall thickness, and regional wall motion. Current medical vision-language models (VLMs) cannot reliably derive quantitative measurements from multidimensional cine images without analysis tools. We present CineMR, a tool-augmented VLM that invokes cardiac image-analysis tools and integrates their outputs into interleaved reasoning for quantitative CMR assessment. We also construct a multi-cohort visual question answering benchmark covering quantitative metric extraction, multiclass diagnosis, and differential diagnosis, together with tools for segmentation, phase selection, volumetry, morphometry, and regional wall motion analysis. CineMR is trained with supervised fine-tuning (SFT) on tool-interaction traces followed by Group Relative Policy Optimization (GRPO) with conditional tool-use rewards. On the multi-cohort cine CMR benchmark, CineMR achieves 35.9% pass@1 and 58.9% pass@4, compared with 1.5% pass@1 for the Qwen3-VL-8B backbone and 0.0% and 7.0% pass@1 for LLaVA-Med v1.5 and MedGemma-4B, respectively. Correct tool invocation reaches 99.8% after GRPO, up from 78.9% after SFT. Live tool outputs improve ventricular measurement accuracy by 20.4--23.7% over direct model predictions, and removing all tools reduces pass@1 from 35.9% to 27.9%. These results highlight the importance of reliable tool use for quantitative cine CMR reasoning and support CineMR as a promising approach for assistive cardiac image assessment. Code, benchmark resources, and model weights are available at https://github.com/AI-MIND-Lab/CineMR.

Cardiac magnetic resonance imaging (CMR) enables assessment of cardiac anatomy, ventricular function, and myocardial tissue characteristics. Clinicians interpret these images by identifying cardiac structures and focusing on the regions relevant to each clinical question, motivating anatomically guided vision-language models (VLMs). Yet CMR-specific supervision for anatomical localisation and clinical question answering remains limited. To address this gap, we investigate fine-grained CMR visual question answering through anatomical grounding and guided attention. We construct 128,915 anatomical-grounding and 42,799 clinical QA pairs across short-axis cine, late gadolinium enhancement, and long-axis cine. These datasets support anatomical recognition, localisation, and clinical assessment without requiring paired reports for individual training images. To help the model learn where to look, we introduce Cardiac Anatomy-Routed Attention (CARA), which selects predicted anatomical priors according to the question and guides decoder attention with learned task-specific strengths. Combining anatomical grounding pretraining with CARA yields our model, CARA-VL. Experiments demonstrate CARA-VL's strengths in clinical assessment and regional localisation across CMR imaging settings, with promising generalization to an external clinical cohort. Together, our data and method provide a practical framework for studying and advancing cardiac visual understanding in VLMs. We will release the QA data derived from public datasets upon publication.

4D flow MRI measures time-resolved, three-directional blood velocity but requires long acquisition times, and its diagnostic signal is carried by the phase difference \emph{between} velocity encodings, not by image magnitude. Recent work has developed a per-encoding variational network to address image reconstruction in this field. In this work, we incorporate a joint supervised and self-supervised training regime and utilize both magnitude and velocity data during supervision. At the same time, we add multiple acquisition-robust and conditioning strategies based on the acceleration factors. On the CMRx4DFlow~2026 aortic dataset (1.5 and 3T), our model lowers RelErr by $38$--$50\%$ and AngErr by $7.0$--$8.7^\circ$ against a training-matched baseline across $R{=}10$--$50$, improving on every held-out subject at every acceleration. Our model also shows strong generalization ability to transfer on out-of-distribution data by employing the joint training scheme, with an increase of $7.2\%$ in SSIM and decrease of $38\%$ and $31\%$ in AngErr and RelErr respectively.

Patient-specific 4D myocardial reconstruction from cine MRI supports quantitative functional assessment, regional motion analysis, and simulation-based modeling. However, routinely acquired short-axis (SAX) cine MRI is sparsely sampled along the through-plane direction, making dense and anatomically consistent surface reconstruction challenging. In this study, we propose an anatomy-aligned surface learning framework that parameterizes the epicardial and endocardial surfaces on a shared circumferential-longitudinal UV domain. This formulation converts irregular 3D reconstruction into structured coordinate-field completion with explicit correspondence across subjects and cardiac phases. Sparse SAX contours are encoded as UV observation fields, coverage-aware sampling improves robustness to incomplete slice coverage, and topology- and distortion-aware learning preserves circumferential continuity and local surface quality. Experiments on three public cine MRI datasets showed that the proposed method consistently outperformed representative mesh-based and implicit reconstruction approaches, achieving overall Chamfer distances of $2.887$~mm on ACDC, $2.641$~mm on M&Ms, and $2.810$~mm on M&Ms-2. The reconstructed sequences also preserved ventricular function, with end-diastolic volume and ejection fraction errors of $3.3$~mL and $1.1 \%$, respectively. These results demonstrate that anatomy-aligned UV learning provides an accurate, efficient, and correspondence-aware representation for sparse cine MRI reconstruction and myocardial modeling. The source code will be available at https://github.com/yuan-xiaohan/SAX2MyoSurf.

Cardiovascular magnetic resonance (CMR) provides comprehensive cardiac assessment but remains underutilized because of the complexity of acquisition, post-processing, and interpretation. Existing artificial intelligence (AI) methods address isolated tasks, limiting clinical integration. We present ORION-CMR (On-scanner Reporting with Integrated fOunda-tioN Model), the first clinically evaluated scanner-native end-to-end CMR foundation model. Pretrained on 12,896,733 CMR images from 9,258 studies, ORION-CMR performs sequence classification, ventricular function assessment, late gadolinium enhancement (LGE) detection, binary and multiclass disease classification, and local large language model-based report generation in approximately 90 seconds. The framework. was evaluated on public benchmarks and clinically validated in a multi-vendor cohort of 68 subjects with normal examinations, congenital heart disease, dilated cardiomyopathy, and myocardial infarction. ORION-CMR outperformed supervised baselines and the previously published CMR foundation model (CMR-FM), achieving state-of-the-art performance for LGE classification and scar segmentation. Clinical evaluation achieved an AUC of 0.96 for normal-versus abnormal classification and 0.88 for multiclass disease classification, while generated reports demonstrated 81.4% agreement with expert interpretation. These results demonstrate the feasibility of real-time scanner-native AI-assisted CMR analysis and automated report generation.

Single Ventricle Physiology (SVP) is a rare subtype of congenital heart disease characterized by the presence of a single functional cardiac ventricle with atypical anatomic configurations that challenge conventional image segmentation approaches. The scarcity of clinical data and the morphological diversity across SVP subtypes make the development of robust segmentation methods particularly difficult. To address these limitations, we propose a cardiac MRI segmentation framework focused on ventricular chambers and myocardium segmentation tailored for SVP. First, we introduce a data augmentation pipeline that generates synthetic 3D cardiac meshes using SDF4CHD and corresponding synthetic cardiac MRI through generative modeling. Second, we introduce SV-Cine, a diagnosis-conditioned adaptation of the foundation model CineMA that incorporates patient-level diagnostic information through Feature-wise Linear Modulation layers, enabling diagnosis-aware feature adaptation during segmentation. We evaluated the framework on an internal cohort with varying SVP subtypes. SV-Cine achieved median Dice scores of 0.89 (IQR: 0.80--0.91) for the left ventricle and 0.72 (IQR: 0.54--0.84) for the right ventricle, outperforming the strongest baseline, nnU-Net, by 0.39 Dice points on right ventricle segmentation. It also yields a median ejection fraction error of 5.55 percentage points (IQR: 3.41--7.69) for the dominant ventricle. Compared with the internal cohort, LV and myocardium segmentation performance was lower for the external cohort; whereas RV Dice scores were comparable for both cohorts. Our findings suggest that a pretrained foundation model can be adapted for highly specialized downstream tasks through usage of diagnosis priors while leveraging anatomic knowledge learned from large-scale MRI datasets during pretraining.

Reconstructing a three-dimensional left-ventricular (LV) endocardial surface from cardiac magnetic resonance (CMR) data is challenging when supervision is available on only a small number of axial slices. Through-plane geometry is weakly constrained, and automatically generated two-dimensional masks can propagate segmentation errors into the recovered shape. We present MR-RS-SDFR, a per-case implicit signed distance field (SDF) framework that reconstructs a continuous LV surface from a CMR volume and sparse axial weak masks. The method first builds a cross-slice SDF initialization from axial and longitudinal geometric cues and then refines the field using two complementary signals: MRI edge-field normal alignment, which provides an image-derived boundary cue independent of the weak masks, and differentiable reslice Dice and contour consistency, which preserve agreement with the observed planes. We evaluate three weak-mask generators -- LOO TransUNet, LOO nnU-Net, and an off-the-shelf Medical SAM3 model used without MM-WHS-specific training or fine-tuning -- and five sparsity levels from 4 to 64 axial planes. In the sparse-16 setting, final MR-RS-SDFR reconstruction reaches 0.928 Dice and 3.80mm HD95 with Medical SAM3 masks. The upstream generators do not exhibit a single common ranking across 2D and dense 3D segmentation, and nnU-Net- and Medical-SAM3-driven sparse reconstruction achieve the same mean final Dice despite different upstream error profiles. Across all three sparse-16 mask sources, MR-RS-SDFR is numerically better than protocol-matched full GHD+DVS in both Dice and HD95. Final Dice improves markedly from sparse-4 to sparse-16 and then saturates at the reported precision through sparse-64. These results support MRI-guided per-case SDF refinement as a reconstruction strategy that remains effective across weak-mask generators and supervision densities.

Cardiac magnetic resonance (CMR) imaging provides complementary information on cardiac anatomy, function, and tissue characterization across multiple sequences and views. In this work, we investigate foundation model pretraining for 2D CMR and introduce CMRVision, a CMR-specific foundation model trained using DINOv3-style self-supervised learning on a multi-center, multi-sequence cohort of 36 million CMR images. We systematically evaluate architectural and training design choices for domain-specific pretraining. CMRVision is evaluated on two downstream tasks: multi-task segmentation across cine, late gadolinium enhancement (LGE), and mapping sequences, and cine view classification. Our experiments show that CMR-specific pretraining, smaller patch sizes, and patch-level objectives consistently improve downstream performance. Across a multi-task segmentation benchmark, CMRVision achieved the strongest overall performance, outperforming prior natural-image (NI), medical-image, supervised, and CMR foundation model baselines. Improvements were modest but consistent across structures and sequences, with Dice scores ranging from 0.940-0.967 for LV and 0.855-0.905 for myocardium, and reaching 0.929 for RV, 0.920 for LA, and 0.931 for RA. The largest gains were observed for myocardium segmentation in LGE and mapping images. In a zero-shot segmentation task on unseen LGE long-axis views, the model achieved an average Dice score of 0.692, demonstrating cross-view generalization. For cine view classification, CMRVision achieved the highest average accuracy (0.906), compared to prior methods reported in the literature. These results highlight the potential of CMRVision to support robust and generalizable cardiac MRI analysis across multiple sequences and views.

Cardiac magnetic resonance imaging (CMR) produces rich sequential data such as temporal cine videos and spatial LGE/mapping stacks, yet most deep learning approaches process individual 2D slices, discarding this context. We present MR-JEPA, a self-supervised video foundation model for CMR that extends LeJEPA to 3D spatiotemporal inputs through tubelet tokenization, spatiotemporal masking augmentation, and initialization from a 2D CMR foundation model. Unlike prior CMR video models limited to cine data, MR-JEPA is pretrained on multi-sequence data (cine, LGE, mapping) from 10,505 patients across two centers without annotations. We evaluate the frozen encoder on six downstream tasks using a unified multi-view gated attention architecture: LV ejection fraction, RV ejection fraction, three myocardial strains (GLS, GCS, GRS), and four-class disease detection. MR-JEPA outperforms other compared methods on all five regression tasks, including both a domain-specific CMR model pretrained on more data with text supervision and a natural-video foundation model, achieving an LV EF MAE of 4.79% (r =0.764) and a GLS MAE of 1.87 (r=0.805), with 21-27% MAE reductions over baselines on strain tasks. For disease detection, MR-JEPA achieved a macro AUG of 0.868, remaining competitive with the domain-specific baseline despite using a fully self-supervised pretraining objective. These results demonstrate the potential of a unified video encoder for robust, multi-view utilization of diverse CMR sequences in clinical cardiac quantification and diagnosis.

Quantifying myocardial perfusion from cardiac magnetic resonance (CMR) can be achieved by fitting tracer-kinetic models to the dynamic contrast-enhanced MR data. However, fitting the observed data with multi-compartment exchange models, which describe the evolution of the contrast agent in the tissue, to estimate perfusion parameters is a challenging inverse problem that is sensitive to noise and acquisition variability. Previously, physics-informed neural networks (PINNs) have been proposed as an alternative to conventional non-linear least squares fitting methods with promising results for quantitative perfusion CMR. In this work, we extend the previously proposed PINN framework with spatiotemporal implicit neural representations (INRs) to represent the MR signal as a continuous spatiotemporal function and to improve the accuracy, smoothness, and physical consistency of the PINN model. In realistic simulated CMR datasets, our proposed PINN with INRs demonstrates improved robustness and parameter estimation accuracy over the previously established methods. The code is available at https://github.com/q-cardIA/pinn-inr.

Foundation models have shown strong transferability in cardiac MRI (CMR), but their effectiveness for heterogeneous multi-view and multi-sequence CMR analysis remains unclear. In this work, we explore the effectiveness of fine-tuning and combining different CMR foundation models for the Universal Multi-Sequence, Multi-Center and Multi-View CMR Segmentation (CMR-Multi) Challenge. CineMA was fine-tuned for cine and late gadolinium enhancement (LGE) segmentation across short-axis and long-axis views. For direct left-ventricular ejection fraction (LVEF) estimation, we used two recent frozen CMR foundation models to extract embedding vectors that were then combined using attention-based multiple-instance learning for LVEF regression. In the challenge validation set, cine segmentation achieved Dice scores of 0.862, 0.883, and 0.902 for short-axis, two-chamber and four-chamber cine MRI, respectively. LGE segmentation achieved Dice scores between 0.621 and 0.846 across views. The direct LVEF regression model achieved an MAE of 4.96 percentage points and a Pearson correlation of 0.91. These results indicate that foundation models can be effectively adapted and combined for multi-view CMR analysis, while accurate LGE scar segmentation remains a challenging task.

Myocardial strain analysis of cardiac magnetic resonance (CMR) images provides an important tool for evaluating cardiac function. However, current techniques require either human-adjusted post-processing with suboptimal regional accuracy, or specialized acquisitions with limited availability. In this paper, we propose to leverage the power of generative models to synthesize high-quality motion-derived strain values from routinely acquired CMR sequences. Specifically, we develop a novel Brownian bridge diffusion model in motion space to learn the probabilistic mapping between standard CMR motion estimated from widely adopted registration methods and highly accurate motion provided by advanced strain imaging techniques. To promote the fidelity of anatomical structure in the generation process, our model is conditioned on the corresponding CMR images. We validate our method on large-scale multi-center CMR datasets including subjects of paired standard cine CMR and advanced strain imaging acquisitions. Experimental results demonstrate that our framework significantly improves the accuracy of motion prediction and strain analysis from standard CMRs compared to existing learning-based approaches. Our research represents a new paradigm for potentially developing cost-effective, clinically deployable AI tools for cardiac function assessment with enhanced strain accuracy in busy clinical workflows. Our code is publicly available at https://github.com/Rishov-MIA/Brownian-Bridge-strain-analysis.

Clinical acquisition in cardiac magnetic resonance (CMR) imaging involves obtaining cross-sectional planes of the heart along the radial and longitudinal directions. Despite these planes being 2D cross-sectional images of the heart, radiologists understand the 3D spatial and continuous temporal nature of the organ being imaged. The same can not be said about the conventional deep learning architectures used to process CMR images, which rely on in-plane and grid-based operations, and are hence unable to organically integrate information from all imaging planes. This paper builds upon previous work on neural implicit segmentation functions (NISF) to overcome unaddressed challenges in cardiac function modeling in the CMR domain. For a given subject, our architecture builds a shared 3D+time representations from all available acquisition planes regardless of orientation. By design, predictions along any imaging plane orientation are cross-sections of the same 3D representation, leading to spatio-temporal consistency across all slices. Moreover, our architecture makes the rotation and translation parameters of imaging planes learnable, allowing us to correct for the commonplace respiratory and patient motion between slice acquisitions under a rigid assumption. Furthermore, interpolation of intensities and segmentation can be performed in 4D at any desired resolution. We perform our study on a 120 subject sub-cohort of CMR imaging data from the UK-Biobank. Our in-plane segmentation performance is on-par with existing CMR segmentation methods and explore how the majority of failure cases arise from limitations in the ground-truth segmentation, for which our representations make predictions with better anatomical accuracy than its original training data. We also evaluate our motion-correction capabilities, displaying quantitative and qualitative improvements in slice alignment.

Accurate estimation of left ventricular (LV) orientation is essential for cardiac magnetic resonance (CMR) imaging and downstream analysis. Existing methods typically formulate orientation recognition as discrete view classification or rely on multi-slice geometric intersection, limiting their ability to model continuous 3D orientation and generalize across arbitrary slices. This work introduces a novel paradigm: Joint LV localization and 3D orientation estimation from a single CMR slice. To investigate this setting, representative orientation-aware detection frameworks are adapted to the CMR domain, and their limitations are analyzed. Upon that, we propose the Polar-Coupled Circular (PCC) embedding that provides a continuous and unambiguous orientation representation to address the limitations. Meanwhile, a scalable benchmark is constructed through automatic slice sampling from volumetric CMR segmentation datasets. Extensive experiments on four datasets demonstrate strong performance, achieving an average mIoU of 86.18% and an average angle deviation of 3.39°. This study establishes a new task setting for single-slice LV orientation modeling and provides a geometry-consistent framework for spatially informed CMR analysis. Code is available at https://github.com/yuyi1005/cmr-3d-ood.

Aims: Cardiovascular magnetic resonance (CMR) imaging enables non-invasive assessment of myocardial structure, function, and pathology, but requires substantial experience in interpretation of CMR images that could be supported by artificial intelligence (AI)-based models. However, use of AI models for enhanced CMR reading is limited by labor-intensive data curation, suboptimal model performance, and unclear implementation pathways. Methods and results: We developed an automated data curation pipeline for CMR-based cardiovascular disease (CVD) diagnosis, integrating open-source locally-run large language models (LLMs) to extract diagnostic labels from narrative CMR reports and preprocessing multimodal imaging data, including cine and late-gadolinium-enhancement (LGE) CMR sequences. Three vision foundation models (DINO, VST, UMedPT) were fine-tuned across these modalities in a two-stage approach. The dataset comprised hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), ischemic cardiomyopathy (ICM), cardiac amyloidosis (CA), and normal controls (NOR). A total of 988 curated cases were randomly divided into 742 for training and 246 for validation. Fine-tuned AI-models achieved high discriminative diagnostic performance on an independent test set comprising 1067 patients , with individual AUC-ROC values of up to 0.937 for the correct diagnosis of HCM and 0.945 for cardiac amyloidosis. Ensemble strategies combining multiple models and modalities further improved AI-based diagnostic accuracy and robustness, achieving the highest overall diagnostic performance for HCM (AUC=0.959, CI [0.936-0.978]), CA (AUC=0.966, CI [0.939-0.986]), NOR (AUC=0.872, CI [0.852-0.894]), DCM (AUC=0.848, CI [0.808-0.885]) and ICM (AUC=0.840, CI [0.809-0.868]). All training and inference code, along with the trained model weights, are publicly available on https://github.com/sinaamirrajab/CMR_CVD.

Clinical cardiac MRI is commonly acquired with high in-plane resolution but coarse through-plane resolution to reduce scan time and accommodate breath-hold and cardiac-motion constraints, which limits 3D analysis and diagnostic accuracy. We propose STRMSR, a reference- and memory-guided through-plane super-resolution (SR) framework that reconstructs high-resolution (HR) cardiac volumes by leveraging HR reference views acquired from the same subject and intermediate SR results as the memory. Our method uses coarse-to-fine contextual matching to establish robust correspondence between low-resolution target and reference/memory images under spatial misalignment. A learnable patch-wise dynamic feature aggregation module predicts content-adaptive mixture weights for each local patch, effectively fusing dynamic information while suppressing unreliable feature transfers. The intermediate SR results stored in the memory bank ensure slice-to-slice consistency for the super-resolved 3D volume. Experiments on the WHS cardiac MRI dataset under two reference protocols, orthogonal-plane views and long-axis chamber views, demonstrate consistent improvements over baselines at 4x and 8x upsampling factors.

Deformable shape representations have proven to be robust complements to texture features in cardiac image classification, offering geometric priors that are invariant to imaging artifacts and intensity variations. However, existing deep networks perform simple concatenation to combine these distinct feature representations, which neither fully exploits their complementary nature nor learns cross-modal feature dependencies. Furthermore, this results in uniform attention across all timepoints; hence ignoring the varying diagnostic importance across the cardiac phases. In this paper, we propose a novel cardiac video classification model that, for the first time, learns temporal features in an integrated space of deformable shape and image texture representations. In particular, we design a bi-directional cross-attention in the latent space to fuse latent deformable shape and image features, allowing each modality to adaptively weight the other based on spatio-temporal correspondence. In contrast to current methods that apply uniform weighting across all the cardiac phases, our approach learns to dynamically adjust the contributions of shape and texture representations, derived from images, over time. We demonstrate state-of-the-art classification performance on a cine cardiac magnetic resonance (CMR) video dataset, achieving improved interpretability from attention mechanisms that identify diagnostically critical cardiac phases and modality contributions.

We propose Bi-PT, a pipeline for reconstructing 3D four-chamber human heart meshes from clinical sparsely sampled cardiac magnetic resonance imaging (CMR) data. This work addresses the error-prone generation of 3D cardiac shape from a sparse point cloud (SPC) extracted from 2D long-axis and short-axis views used in routine clinical CMR protocols. Bi-PT enables accurate inference of the four-chamber heart mesh from the SPC by learning robust point features via bidirectional point cross-attention between an atlas and the SPC, together with per-point semantic labels that improve correspondence estimation. We formulate the deformation field as a Neural Ordinary Differential Equation (NODE) parameterized by a per-point affine transformation and translation to deform the atlas toward the target heart shape. By learning such a NODE, we can guarantee the deformation field to be a locally affine diffeomorphic deformation. We also integrate a semantic label loss into the Chamfer distance to encourage label-consistent correspondences and add a smoothness regularization to stabilize and improve the learning of the deformation field. Extensive experiments demonstrate that Bi-PT achieves accurate and robust performance compared to baselines.

Cardiac cine Magnetic Resonance Imaging (MRI) is a critical diagnostic tool that provides dynamic insights for radiologists. To accelerate acquisition, under-sampled k-space data is often used, requiring reconstruction methods that combine coil sensitivity encoding with prior information to recover missing data. Deep learning approaches have gained more attention for leveraging data-adaptive priors. While supervised learning approaches are a common choice, they depend on fully sampled reference data, which is not always available. Unsupervised methods eliminate the need for fully sampled reference data, which can be advantageous in cardiac cine MRI reconstruction. Among them, implicit neural representations (INRs) have shown great potential due to their simple architecture and good quality reconstructions. In this work, we propose an image-domain dual-branch INR framework, termed I-FP-INR, which extends the original INR design by introducing an additional feature-processing branch. This design aims to extract complementary feature embeddings to enhance the overall representation, thereby benefiting reconstruction. Extensive evaluations on both public datasets and in-house data show consistent improvements over baseline methods in reconstruction quality, with strong robustness across varied scenarios.

Real-time cardiac cine MRI enables visualization of the beating heart during free breathing, but severe undersampling and motion make reconstruction highly challenging. A central challenge for reconstruction is incorporating powerful priors of cardiac anatomy while remaining computationally efficient. We propose Piecewise Dynamic Diffusion Regularization (PDDR), a reconstruction method that integrates a spatiotemporal diffusion model as a generative prior within a variational reconstruction framework for cine MRI. The model employs dedicated spatial layers to encode anatomical structure and temporal layers to capture cardiac motion learned from gated cine data. PDDR leverages the dynamic prior in a piecewise manner, enabling the efficient use of spatiotemporal diffusion models for processing of long real-time sequences. Experiments on retrospectively accelerated and prospective real-time cine MRI demonstrate that PDDR outperforms classical, unsupervised, and diffusion-based methods, delivering high-quality reconstructions with substantially reduced computation time compared to state-of-the-art baselines. These results highlight PDDR as a practical and scalable solution for free-breathing, real-time cardiac MRI. Code is available at https://github.com/MLI-lab/pddr.

Accurate 4D whole-heart mesh reconstruction from sparse cine MRI is critical for creating cardiac digital twins, but remains challenging due to limited 2D slice coverage and the complex coupling between cardiac shape and motion. Existing methods often rely on intermediate contour fitting and typically reconstruct static, single-phase, or partial cardiac geometries, limiting their ability to capture full-chamber dynamics. We propose a novel end-to-end framework for reconstructing temporally resolved whole-heart meshes from multi-view 2D cine MRI sequences by learning an image-to-mesh mapping. The framework incorporates a differentiable contour renderer inspired by the Beer-Lambert attenuation principle, enabling anatomy-aware supervision of 3D+t mesh deformation through contour-based projection losses. To improve temporal consistency across the cardiac cycle, we further introduce a multi-scale temporal modeling module that integrates global cycle-level dynamics with local inter-frame coherence to generate smooth and physiologically plausible mesh trajectories. The proposed method achieved a whole-heart mean absolute error of 1.68 $\pm$ 0.31 mm and a motion jitter of 0.77 $\pm$ 0.17 $\mathrm{mm}/\mathrm{frame}^{3}$, outperforming existing methods with lower reconstruction error and substantially improved motion smoothness. It also improved 2D contour alignment across multiple cine MRI views and supported downstream proof-of-concept electrophysiological simulation. The code will be released publicly upon acceptance of the manuscript for publication.

Implicit neural representations (INRs) are well suited to cardiac motion estimation, providing continuous, compact representations of motion fields. However, fitting an INR to each image sequence is time-consuming and sensitive to the optimisation trajectory. Learned priors can help guide optimisation towards plausible motion fields and enable faster adaptation, but learning priors for cardiac motion INRs remains under-explored. In this work, we compare four strategies for learning cardiac motion priors, including a population prior learned by joint optimisation, a consensus prior obtained by weight averaging, auto-decoders, and meta-learning. Using short-axis tagged cardiac magnetic resonance images from the UK Biobank, we evaluate their impact on tracking accuracy, motion behaviour, and adaptation trajectory. All learned priors substantially improved early adaptation performance compared with random initialisation. While the simple consensus prior was effective, auto-decoders recovered large deformations faster during early adaptation. Meta-learning achieved strong early performance and maintained the best adaptation trajectory over 50 iterations.

Cardiac magnetic resonance imaging (CMR) routinely records structured acquisition metadata, yet most CMR foundation models rely primarily on image-only pre-training and leave this naturally available source of weak semantic supervision largely underexplored. We propose MetaCLIP-CMR, a metadata-driven framework based on Contrastive Language--Image Pre-training (CLIP), which converts imaging modality, anatomical view, scanner vendor, field strength, and scanner model into textual supervision for CMR representation learning. The pretrained image encoder is evaluated on imaging modality classification, cine view classification, and cardiac segmentation. MetaCLIP-CMR achieves 86.8% modality accuracy and 86.5% cine view accuracy, clearly outperforming ImageNet and masked reconstruction initialisations. For downstream cardiac segmentation, MetaCLIP-CMR consistently obtains the highest Dice score across the evaluated ACDC and M&Ms cine short-axis (SAX) settings under both full-data and 20% fine-tuning regimes. Compared with recent image-focused large-scale CMR pre-training models, MetaCLIP-CMR achieves comparable ACDC segmentation performance, while requiring less than 1% of their pre-training image scale. These results suggest that metadata learning offers a natural and easy-to-use strategy for transforming routinely recorded acquisition information into effective supervision for foundation-level CMR representation learning, highlighting the promise of metadata-driven multimodal pre-training.

Developing robust artificial intelligence models for 4D (3D + time) medical imaging is constrained by limited annotated data, inter-device domain shifts, and privacy restrictions. To address this, we propose a 4D controllable generative framework for anatomically consistent data augmentation. A semi-supervised variational autoencoder learns a compact latent representation of anatomical volumes while jointly predicting aligned segmentation masks in a unified framework. Anatomical structure is then disentangled from temporal dynamics through a cascaded latent diffusion model (LDM). A static LDM generates subject-specific anatomy conditioned on clinical priors (diagnosis and volumes measures) and a subsequent motion LDM estimates residual latent motions, ensuring strict temporal coherence across the 4D sequence. The proposed approach was evaluated on cine cardiac MRI as a representative 4D imaging application. Experiments across multiple datasets demonstrate high controllability of static anatomy (Pearson r > 0.8) and strong temporal coherence (FVD = 288.08). In cross-vendor generalization experiments, augmenting training sets with synthetic 4D sequences significantly improves downstream segmentation performance. Using nnU-Net, the proposed augmentation strategy improves the average Dice score by 1.4% and reduces the Hausdorff Distance by 3.0mm compared to training on real data alone, for the left ventricle, Dice improves by 2.8% with a 5.4mm reduction in boundary error. Overall, this framework provides a scalable and controllable solution for 4D medical image synthesis, supporting the development of more robust models with limited annotations and cross-vendor variability. Code available on https://github.com/cyiheng/4DCardiacMRISynthesis.

Cardiac magnetic resonance imaging (CMR) captures rich spatiotemporal information about ventricular structure and motion, but conventional risk models use only a few image-derived indices from selected cardiac phases. We present a latent dynamical model that encodes bi-ventricular anatomy and full-cycle cine motion as a continuous latent trajectory, using heart-rate-aware neural ordinary differential equation (ODE) dynamics and a graph-based mesh autoencoder to reconstruct anatomically consistent 3D+t ventricular motion. A covariate-conditioned prior defines the expected end-diastolic latent state, and a Cox proportional hazards model tests whether deviations from this prior predict incident heart failure. We studied 72,386 UK Biobank participants without baseline cardiovascular disease, including 367 incident heart failure events. In a held-out evaluation subset, adding the latent score to refitted pooled cohort equations improved the stratified C-index from 0.704 to 0.785, compared with 0.764 for seven established cardiac markers. Compared with non-graph and non-ODE approaches, the proposed model gave the best trade-off between reconstruction fidelity, generative realism, and downstream prognostic performance. These results suggest that continuous full-cycle modeling of ventricular motion provides informative cardiac phenotypes beyond conventional CMR summaries, while external validation in more representative patient cohorts is required before clinical risk-prediction use.

Cine cardiac magnetic resonance is the gold standard for assessing cardiac function, but the scarcity of public datasets limits the development of advanced data-driven models. To address this limitation, we propose a generative method for synthesizing temporally coherent and anatomically consistent cardiac sequences. Our text-to-video framework decouples cardiac spatial structure from temporal motion. First, a fine-tuned diffusion model synthesizes an initial frame from a clinical text prompt, controlling anatomical features. Then, a latent flow model conditioned on a cardiac phase embedding generates the complete cardiac motion, ensuring spatial consistency and temporal control. Our model generates anatomically and pathologically diverse sequences with high temporal coherence and strong fidelity to input prompts, achieving a FID of 31.68 for image realism and a CLIP score of 31.04 for text-image alignment. These experimental results highlight its potential to produce high-fidelity, on-demand medical data, offering a scalable solution to data scarcity.